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Conrad L. Schoch

Bio: Conrad L. Schoch is an academic researcher from National Institutes of Health. The author has contributed to research in topics: Dothideomycetes & Phylogenetic tree. The author has an hindex of 52, co-authored 93 publications receiving 22018 citations. Previous affiliations of Conrad L. Schoch include Cornell University & Oregon State University.


Papers
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Journal ArticleDOI
01 Dec 2017
TL;DR: This article focuses on one such step by proposing a standard way for publications to flag papers with novel taxonomic information, so the potential for automated searches of publication aggregators are improved, as well as the accurate curation ofTaxonomic information.
Abstract: The combination of manual curation and the reliance on updates from submitters to the public sequence databases is currently inefficient and impedes the comprehensive and timely release of records with new taxonomic names. This should be improved by making several steps during data release more efficient. This article focuses on one such step by proposing a standard way for publications to flag papers with novel taxonomic information. As a result, the potential for automated searches of publication aggregators are improved, as well as the accurate curation of taxonomic information.

10 citations

Journal ArticleDOI
TL;DR: Hypogymnia minilobata is described as a new species of lichenized fungi from the coast of southern California and the Channel Islands that is distinguished from that species by its small size, consistently appressed growth form, slightly smaller and more elongate spores, and distinct ITS and GPD sequences.
Abstract: Hypogymnia minilobata is described as a new species of lichenized fungi from the coast of southern California and the Channel Islands. Previously lumped under H. occidentalis, H. minilobata is distinguished from that species by its small size, consistently appressed growth form, slightly smaller and more elongate spores, and distinct ITS and GPD sequences. So far H. minilobata is known from coastal scrub and woodlands, and is especially common in the Los Osos and Baywood areas of San Luis Obispo County, California.

10 citations

Book ChapterDOI
01 Jan 2015
TL;DR: This review describes the latest taxonomic classifications substantiated with DNA and protein sequence comparisons and discusses morphology, biology, and ecology within this context.
Abstract: The modern concepts of Dothideomycetes and Arthoniomycetes can be traced back to Luttrell (Mycologia 47:511–532, 1955) who, relying on data from a number of previous publications, combined lichenized and nonlichenized fungi in a single class, Loculoascomycetes A current concept of two separate classes, as well-defined sister taxa, is still new, but it is closely tied to the use of DNA-sequence-based phylogenies to define fungal taxa DNA sequence comparisons, which have now been in use in mycology since the early 1990s, confirmed that important morphological and developmental characters traditionally used in the taxonomy of loculoascomycetes are homoplasious What was earlier referred to as the bitunicate ascomycetes contains multiple diverse lineages, which have now been placed in three different classes within Ascomycota The class Eurotiomycetes contains Pyrenulales, Verrucariales, and Chaetothyriales within subclass Chaeothyriomycetidae (Geiser et al Mycologia 98:1053–1064, 2006) and the remaining (and majority of) bitunicate species reside within two sister classes, Arthoniomycetes and Dothideomycetes This review describes the latest taxonomic classifications substantiated with DNA and protein sequence comparisons and discusses morphology, biology, and ecology within this context

10 citations

Journal ArticleDOI
TL;DR: Microscopic studies showed that cell division of the kar3 mutants was impaired and NaCl-stress conditions aggravated the phenotype, pointing to a possible specific involvement of KAR3 in the osmotic-stress response.
Abstract: Several mutants of Saccharomyces cerevisiae showing poor growth in the presence of elevated concentrations of NaCl were isolated to identify genes involved in the osmo-stress response. One of these mutants (WAY.5-4A-11; osr11) which showed a clear 2:2 segregation of the salt-stress phenotype upon tetrad analysis when crossed to a wild-type strain has been characterised. The mutation responsible for poor growth under salt-stress was recessive. The corresponding gene was cloned by complementation of the mutant phenotype and a 3.5-kb fragment was isolated. The sequence of this fragment matched that of KAR3, a gene previously identified to be involved in karyogamy and mitosis. Allelism of OSR11 to KAR3 was confirmed by tetrad analysis, and disruption mutants showed the same NaCl-phenotype as the original osr11 mutation. The disruption mutant was more sensitive to high sucrose concentrations than the original mutant was to high glucose concentrations. In a different genetic background (W303-1A), the kar3 disruptants were less sensitive to osmo-stress than the WAY.5-4A strain. Heat-stress, nitrogen-starvation and cultivation on ethanol failed to affect the growth of osr11 and kar3 mutants, pointing to a possible specific involvement of KAR3 in the osmotic-stress response. Microscopic studies showed that cell division of the kar3 mutants was impaired and NaCl-stress conditions aggravated the phenotype.

8 citations

Journal ArticleDOI
TL;DR: Three relatively well-defined genetic groups and one residual group in the H. imshaugii complex were detected with haplotype networks based on the ITS locus; however, phylogenetic reconstructions on combined ITS, mtSSU, GPD1 and TEF1 loci did not reflect this pattern, and there has insufficient evidence to support defining any of these groups as new taxa.
Abstract: Hypogymnia imshaugii is one of the most common, conspicuous and morphologically variable epiphytic lichens of the Pacific coastal states and provinces. The species varies greatly in morphology and chemistry, suggesting multiple closely related species or one or more phenotypically plastic species. We sought to determine whether additional ecologically meaningful species might be present within the H. imshaugii complex. Improving our species concepts could potentially improve ecological inferences based on community sampling. Three relatively well-defined genetic groups and one residual group in the H. imshaugii complex were detected with haplotype networks based on the ITS locus; however, phylogenetic reconstructions on combined ITS, mtSSU, GPD1 and TEF1 loci did not reflect this pattern. At present, we have insufficient evidence to support defining any of these groups as new taxa. The four major chemotypes in H. imshaugii differed in frequency among the genetic groups. None of the genetic groups...

8 citations


Cited by
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Journal ArticleDOI
23 Jan 2014-Nature
TL;DR: Increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease.
Abstract: Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.

7,032 citations

Journal ArticleDOI
Minoru Kanehisa1, Miho Furumichi1, Mao Tanabe1, Yoko Sato2, Kanae Morishima1 
TL;DR: The content has been expanded and the quality improved irrespective of whether or not the KOs appear in the three molecular network databases, and the newly introduced addendum category of the GENES database is a collection of individual proteins whose functions are experimentally characterized and from which an increasing number of KOs are defined.
Abstract: KEGG (http://www.kegg.jp/ or http://www.genome.jp/kegg/) is an encyclopedia of genes and genomes. Assigning functional meanings to genes and genomes both at the molecular and higher levels is the primary objective of the KEGG database project. Molecular-level functions are stored in the KO (KEGG Orthology) database, where each KO is defined as a functional ortholog of genes and proteins. Higher-level functions are represented by networks of molecular interactions, reactions and relations in the forms of KEGG pathway maps, BRITE hierarchies and KEGG modules. In the past the KO database was developed for the purpose of defining nodes of molecular networks, but now the content has been expanded and the quality improved irrespective of whether or not the KOs appear in the three molecular network databases. The newly introduced addendum category of the GENES database is a collection of individual proteins whose functions are experimentally characterized and from which an increasing number of KOs are defined. Furthermore, the DISEASE and DRUG databases have been improved by systematic analysis of drug labels for better integration of diseases and drugs with the KEGG molecular networks. KEGG is moving towards becoming a comprehensive knowledge base for both functional interpretation and practical application of genomic information.

5,741 citations

Journal ArticleDOI
TL;DR: The changes that have occurred in CAZy during the past 5 years are outlined and a novel effort to display the resolution and the carbohydrate ligands in crystallographic complexes of CAZymes is presented.
Abstract: The Carbohydrate-Active Enzymes database (CAZy; http://www.cazy.org) provides online and continuously updated access to a sequence-based family classification linking the sequence to the specificity and 3D structure of the enzymes that assemble, modify and breakdown oligo- and polysaccharides. Functional and 3D structural information is added and curated on a regular basis based on the available literature. In addition to the use of the database by enzymologists seeking curated information on CAZymes, the dissemination of a stable nomenclature for these enzymes is probably a major contribution of CAZy. The past few years have seen the expansion of the CAZy classification scheme to new families, the development of subfamilies in several families and the power of CAZy for the analysis of genomes and metagenomes. This article outlines the changes that have occurred in CAZy during the past 5 years and presents our novel effort to display the resolution and the carbohydrate ligands in crystallographic complexes of CAZymes.

4,997 citations

Journal ArticleDOI
TL;DR: Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation.
Abstract: Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

4,116 citations

Journal ArticleDOI
TL;DR: The approach to utilizing available RNA-Seq and other data types in the authors' manual curation process for vertebrate, plant, and other species is summarized, and a new direction for prokaryotic genomes and protein name management is described.
Abstract: The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.

4,104 citations